Alternatives and similar repositories for GNNome-assembly

Users that are interested in GNNome-assembly are comparing it to the libraries listed below

• lbcb-sci / GNNome
  A framework for training graph neural networks to untangle assembly graphs obtained from OLC-based de novo genome assemblers.
  ☆48Updated last month
• bcgsc / ntEmbd
  Deep learning embedding for nucleotide sequences
  ☆19Updated 7 months ago
• Weeks-UNC / RNAvigate
  Very flexible tools for plotting and analyzing all kinds of RNA structure data
  ☆14Updated 4 months ago
• OATML / EVE
  Official repository for the paper "Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning". Jo…
  ☆65Updated 3 years ago
• kaistsystemsbiology / DeepProZyme
  DeepECtransformer
  ☆28Updated 2 years ago
• allydunham / sequence_unet
  Fully convolutional deep learning variant effect predictor architecture
  ☆23Updated last year
• JJAlmagro / TargetP-2.0
  Detecting Sequence Signals in Targeting Peptides Using Deep Learning
  ☆13Updated 6 years ago
• althonos / pytrimal
  Cython bindings and Python interface to trimAl, a tool for automated alignment trimming. Now with SIMD!
  ☆27Updated 2 months ago
• TattaBio / DGEB
  Diverse Genomic Embedding Benchmark
  ☆48Updated 2 months ago
• liudan111 / EvoMIL
  Prediction of virus-host association using protein language models and multiple instance learning
  ☆20Updated last year
• moss-lab / ScanFold
  ScanFold is an RNA sequence scanning pipeline which attempts to identify potentially functional RNA secondary structures. This is done by…
  ☆20Updated 2 years ago
• y-hwang / gLM
  Genomic language model predicts protein co-regulation and function
  ☆83Updated 7 months ago
• ayaanhossain / ViennaRNA
  ViennaRNA Package consists of a C code library for the prediction and comparison of RNA secondary structures
  ☆14Updated 3 years ago
• macwiatrak / Bacformer
  Modeling whole bacterial genome as a sequence of proteins.
  ☆77Updated 2 weeks ago
• Chokyotager / ORFFinder
  ORFFinder in Python
  ☆15Updated last year
• Protein-Sequence-Annotation / PSALM
  Protein Sequence Annotation with Language Models
  ☆24Updated 5 months ago
• dnbaker / bioseq
  Tokenizers and Machine Learning Models for biological sequence data
  ☆25Updated last year
• eternagame / EternaFold
  Improving RNA structure prediction through multitask learning on diverse crowdsourced data.
  ☆62Updated last year
• bioinf-mcb / Metagenomic-DeepFRI
  Pipeline for searching and aligning contact maps for proteins, then running DeepFri's GCN.
  ☆40Updated 2 weeks ago
• gagneurlab / dependencies_DNALM
  Code repository for the manuscript: Nucleotide dependency analysis of DNA language models reveals genomic functional elements
  ☆19Updated 7 months ago
• althonos / pyfamsa
  Cython bindings and Python interface to FAMSA, an algorithm for ultra-scale multiple sequence alignments.
  ☆36Updated 3 weeks ago
• minmarg / comer2
  Fast, sensitive and accurate protein remote homology search on GPUs
  ☆16Updated last year
• apcamargo / RNAsamba
  A tool for computing the coding potential of RNA transcript sequences using deep learning classification model
  ☆55Updated 3 years ago
• Benjamin-Lee / CodonAdaptationIndex
  Python Implementation of Codon Adaption Index
  ☆37Updated 2 years ago
• Genentech / regLM
  Toolkit for training hyenaDNA-based autoregressive language models on DNA sequences.
  ☆49Updated last year
• mourisl / MSAplot
  Plot multiple sequence alignment (MSA)
  ☆15Updated last year
• JinsenLi / deepDNAshape
  A method to predict DNA shape features considering farther flanking region.
  ☆36Updated last year
• multimeric / Unipressed
  Comprehensive Python client for the Uniprot REST API
  ☆52Updated last month
• johli / seqprop
  Stochastic Sequence Propagation - A Keras Model for optimizing DNA, RNA and protein sequences based on a predictor
  ☆50Updated last year
• gagneurlab / SpeciesLM
  Species-aware DNA language models capture regulatory elements and their evolution
  ☆25Updated 2 years ago